Ribozymes are essentially RNA molecules that are capable of catalyzing a chemical reaction. Many naturally occurring ribozymes either catalyze the hydrolysis of their own phosphodiester bonds or cause the hydrolysis of bonds in other RNA molecules. They also catalyze the aminotransferase activity of the ribosome.
Researchers have developed synthetic ribozymes in the laboratory that are able to catalyze their own synthesis under specific conditions. One example is the RNA polymerase ribozyme. Using mutagenesis and selection, scientists have managed to develop and improve variants of the Round-18 polymerase ribozyme from 2001.
The best variant so far is called B6.61, which can add up to 20 nucleotides to a primer template over a period of 24 hours, at which point hydrolysis of the ribozyme’s phosphodiester bonds causes it to decompose.
Some examples of naturally occurring ribozymes include:
- RNase P
- Peptidyl transferase 23S rRNA
- GIR1 branching ribozyme
- Group I and Group II introns
- Hairpin ribozyme
- Hammerhead ribozyme
- HDV ribozyme
- VS ribozyme
- Mammalian CPEB3 ribozyme
- CoTC ribozyme
- glmS ribozyme
Since ribozymes have been discovered, the naturally occurring ribozymes have fallen into two main groups: large ribozymes and small ribozymes. Large ribozymes splice flanking sequences together, while small ribozymes cleave conserved sites that exist within their own molecule. One main example of a large ribozyme is the first one to be discovered, which is the Tetrahymena group I intron. Examples of small ribozymes include the hammerhead, the hairpin, the hepatitis delta ribozymes and varkud satellite RNA.
Large ribozymes may have up to 3000 nucleotides and can generate reaction products with a free 3’- hydroxyl and 5’-phosphate group. Small ribozymes on the other hand, usually contain 30 to 150 nucleotides and generate products with a 2’-3’-cyclic phosphate and a 5’-hydroxyl group.